Re: [R] can't install R with *local* gcc
Hello, I infer from your answer that piece of information which is most important for us now: That my configuration instructions for R should work (should be correct). Given all these unspecified build-systems we have to fight (at least Gmp, Mpfr, Gcc with everything in it, R, and finally our own) one first wants to know where obvious errors are. Thanks! Once I know more (we are in the middle of it) I move to the devel-list. Oliver P.S. Currently it seems that the Gcc-build is not correct (still the same with 4.4.5), not propagating linker-information to the building of libraries (while the compiler-builds seem alright). > > Hint #1: Expect the process to be somewhat painful... > Hint #2: Study the configure script and config.log to the level where you can > reproduce the mixed C/Fortran code that it is trying to build and run and > with which commands it is trying to build it > Hint #3: Figure out what it really should have done to build such code > > An alternative hint is first to try setting up a very simple Fortran function > to, say, double a number, and a C main program that calls it. Then try > figuring out the compiler/linker options to make it work. (That is of course > what configure was trying to do in the first place, but doing it by hand > might be less prone to getting multiple toolchains mixed up.) > > > -- > Peter Dalgaard > Center for Statistics, Copenhagen Business School > Solbjerg Plads 3, 2000 Frederiksberg, Denmark > Phone: (+45)38153501 > Email: pd@cbs.dk Priv: pda...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] can't install R with *local* gcc
On Dec 26, 2010, at 17:50 , Oliver Kullmann wrote:
> Hello,
>
> we re-distribute R with our open-source platform
> http://www.ok-sat-library.org/
> where we use R mainly for evaluation of computational experiments.
> Due to the various platforms, we build everything from source, and that works
> fine.
> Until now, that is: there are circumstances (for example in computer-science
> computer labs)
> where no Fortran-compiler is provided, and the users (students) can't change
> that.
> Thus we now try to build gfortran as part of the GCC version 4.2.4 suite, and
> building
> R using that local gcc.
> We already use the local C and C++ compiler of the suite extensively, and that
> all works. But we don't have any experience with using gfortran.
> The gcc-build works fine, everything seems alright --- only R (version
> 2.11.0) won't build with it:
>
> We use the configuration
>
> F77=/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/bin/gfortran
>
> FC=${F77}
> CC=/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/bin/gcc
>
> CXX=/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/bin/g++
>
> LDFLAGS="-L
> /home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/lib"
>
> ./configure
> --prefix=/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/R/2.11.0
>
> (the same problems with "lib64" instead of "lib", by the way)
>
> which yields
>
> checking for Fortran 77 libraries of
> /home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/bin/gfortran...
>
> -L/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/lib
>
> -L/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/lib/gcc/x86_64-unknown-linux-gnu/4.2.4
>
> -L/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../lib64
> -L/lib/../lib64 -L/usr/lib/../lib64
> -L/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../..
> -lgfortranbegin -lgfortran -lm
> /home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/lib/libgfortran.a
>
> which looks alright to me (but I don't know Fortran), but then we get
>
> checking for dummy main to link with Fortran 77 libraries... none
> checking for Fortran 77 name-mangling scheme... lower case, underscore, no
> extra underscore
> checking whether
> /home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/bin/gfortran
> appends underscores to external names... yes
> checking whether
> /home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/bin/gfortran
> appends extra underscores to external names... no
> checking whether mixed C/Fortran code can be run... configure: WARNING:
> cannot run mixed C/Fortran code
> configure: error: Maybe check LDFLAGS for paths to Fortran libraries?
> make: *** [R_base] Error 1
>
> The R installation-documentation doesn't say much on using local compilers
> (more or less nothing), and everything we could
> get from it are the above settings of environment variables.
>
> Internet search reveals old stuff on "libg2c" which appears not to exist
> anymore, some recommendations
> not to build from sources (which is not an option for us), an open Sage
> ticket (apparently without any
> further work on it), and a request to the R-list with apparently no reply.
>
> Since we are working in a well-defined setting (gcc is fully under our
> control), and apparently
> all the libraries needed are build by gcc (though this is nowhere said or
> (dream) specified),
> it should be possible to solve that problem.
>
> I very hope to get some hints (we can't get R running (for our system!)
> otherwise).
> The error is exactly the same on various systems (all 64-bit machines, Intel
> and AMD).
> If we use the system-gcc (4.5.0 or 4.1.2) then the installation of R works
> without problems;
> here (for one of the machines) some data
I suppose r-devel would be a better mailing list for this sort of thing, but
since we're here:
Hint #1: Expect the process to be somewhat painful...
Hint #2: Study the configure script and config.log to the level where you can
reproduce the mixed C/Fortran code that it is trying to build and run and with
which commands it is trying to build it
Hint #3: Figure out what it really should have done to build such code
An alternative hint is first to try setting up a very simple Fortran function
to, say, double a number, and a C main program that calls it. Then try figuring
out the compiler/linker options to make it work. (That is of course what
configure was trying to do in the first place, but doing it by hand might be
less prone to getting multiple toolchains mixed up.)
>
>> version
>
[R] can't install R with *local* gcc
Hello,
we re-distribute R with our open-source platform http://www.ok-sat-library.org/
where we use R mainly for evaluation of computational experiments.
Due to the various platforms, we build everything from source, and that works
fine.
Until now, that is: there are circumstances (for example in computer-science
computer labs)
where no Fortran-compiler is provided, and the users (students) can't change
that.
Thus we now try to build gfortran as part of the GCC version 4.2.4 suite, and
building
R using that local gcc.
We already use the local C and C++ compiler of the suite extensively, and that
all works. But we don't have any experience with using gfortran.
The gcc-build works fine, everything seems alright --- only R (version 2.11.0)
won't build with it:
We use the configuration
F77=/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/bin/gfortran
FC=${F77}
CC=/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/bin/gcc
CXX=/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/bin/g++
LDFLAGS="-L
/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/lib"
./configure
--prefix=/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/R/2.11.0
(the same problems with "lib64" instead of "lib", by the way)
which yields
checking for Fortran 77 libraries of
/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/bin/gfortran...
-L/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/lib
-L/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/lib/gcc/x86_64-unknown-linux-gnu/4.2.4
-L/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../lib64
-L/lib/../lib64 -L/usr/lib/../lib64
-L/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../..
-lgfortranbegin -lgfortran -lm
/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/lib/libgfortran.a
which looks alright to me (but I don't know Fortran), but then we get
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... lower case, underscore, no
extra underscore
checking whether
/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/bin/gfortran
appends underscores to external names... yes
checking whether
/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/bin/gfortran
appends extra underscores to external names... no
checking whether mixed C/Fortran code can be run... configure: WARNING: cannot
run mixed C/Fortran code
configure: error: Maybe check LDFLAGS for paths to Fortran libraries?
make: *** [R_base] Error 1
The R installation-documentation doesn't say much on using local compilers
(more or less nothing), and everything we could
get from it are the above settings of environment variables.
Internet search reveals old stuff on "libg2c" which appears not to exist
anymore, some recommendations
not to build from sources (which is not an option for us), an open Sage ticket
(apparently without any
further work on it), and a request to the R-list with apparently no reply.
Since we are working in a well-defined setting (gcc is fully under our
control), and apparently
all the libraries needed are build by gcc (though this is nowhere said or
(dream) specified),
it should be possible to solve that problem.
I very hope to get some hints (we can't get R running (for our system!)
otherwise).
The error is exactly the same on various systems (all 64-bit machines, Intel
and AMD).
If we use the system-gcc (4.5.0 or 4.1.2) then the installation of R works
without problems;
here (for one of the machines) some data
> version
platform x86_64-unknown-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 2
minor 11.0
year 2010
month 04
day22
svn rev51801
language R
version.string R version 2.11.0 (2010-04-22)
Thanks for you help in any case!
Oliver
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